Feature Article - October 2005
by Do-While Jones

Chimps Are Like Us

The chimpanzee genome has been decoded and compared to the human genome. What did scientists find? They found that the genomes are very similar! What a surprise!

Every time a comparison of human DNA and chimpanzee DNA appears in the technical literature, we pass that information along to you. Our previous essays have been titled “98% Chimp”, “Monkey Business”, and “More Monkey Business”. Since those essays were written, the chimpanzee genome has been completely decoded. The September 1, 2005, issue of Nature was largely devoted to articles analyzing the similarities and differences in human and chimp DNA. The September 2 issue of Science contained an analysis of the September 1 Nature analysis.

In our previous essays, we described how different methods of comparison were used to produce different percentages. The calculated values were 98%, 98.5%, 98.8%, and 99.4%. What’s the “real” value? Well, it still depends on how you measure it.

… the draft sequence was announced but not formally published in 2003. Now the team, led by Robert Waterston of the University of Washington (UW), Seattle, confirms in Nature the oft-cited statistic that on average only 1.23% of nucleotide bases differ between chimps and humans. … The total genetic difference between humans and chimps, in terms of number of bases, sums to about 4% of the genome. That includes 35 million single base substitutions plus 5 million insertions or deletions (indels), says Waterston. 1

Four Percent Difference!

That’s right. Waterston says that the total difference is 4%, which somehow confirms the 1.23% average. We are still trying to figure out that math!

If there really is only 1.23% average difference between human DNA and chimp DNA, how much average difference is there between two different human DNA molecules? Certainly it must be much much less than 1.23%. If that is true, how can DNA evidence be used in a court of law to convict criminals?

The papers confirm the astonishing molecular similarity between ourselves and chimpanzees. The average protein differs by only two amino acids, and 29% of proteins are identical. The work also reveals that a surprisingly large amount of genetic material--2.7% of the genomes--has been inserted or deleted since humans and chimps went their separate evolutionary ways 6 million years ago. 2

DNA contains the biological instructions for making proteins. If 29% of the proteins are identical, that means that 71% are different, doesn’t it? If the DNA is 96% the same, why are 71% of the proteins it produces different?

Seriously, we’re just having fun with the numbers. Clearly human DNA and chimp DNA is very similar. We don’t dispute that. But, as Mark Twain once said [Correction: It might have been Leonard Henry Courtney who said it.], “There are three kinds of lies: Lies; damn lies; and statistics.” Scientists can present whatever numbers they want to emphasize whatever they want. Which numbers are the most important is really a matter of opinion. Evolutionists always present the numbers in such a way as to diminish the difference between humans and chimpanzees to make it more plausible that they have a common ancestor.

Similarity can either be the result of common ancestry or common design. The 96% (or whatever) similarity alone doesn’t prove common ancestry. It might be the result of a designer making two very similar things.

If the similarity is the result of a common ancestor, then one must explain how the differences came about. Evolutionists typically claim the differences came from random mutations, filtered by natural selection. This argument sounded plausible before science discovered DNA, got a better understanding of genetics, and developed the concept of information theory. The evolutionary explanation was plausible before science discovered how many differences there are between species.

It is our opinion that the important numbers are 35 million plus 5 million. That is, if you compare human DNA with chimp DNA, there are 35 million places where the molecules differ, and there are a total of 5 million places where the human DNA either has more or fewer bases than chimp DNA. (That is, there are 5 million places where bases have been “inserted” or “deleted” if one assumes that both kinds of DNA had a common evolutionary origin.) So, there are 40 million differences, total.

Who changed?

"It's frustrating that humans and chimps are so similar," says Andrew Clark of Cornell University in Ithaca, New York. It's difficult to tell whether a DNA sequence in humans that is missing in chimps was really added during human evolution or has simply been lost in the chimp lineage. 3

Remember that evolutionists believe (by faith) that humans and chimpanzees both evolved from an unknown common ancestor about 6 million years ago. If evolutionary rates were the same for both humans and chimps, those 40 million base pair differences should be evenly divided between humans and chimps. In other words, our DNA would have about 20 million differences from the mythical common ancestor, and chimp DNA would have a different 20 million differences. Vain humans, though, would rather believe that the differences are split 30/10 (or 35/5) rather than 20/20 because we are so much more “dramatically” different from the apelike “common ancestor” than chimpanzees are.

In some behavioral and cognitive traits, humans have changed dramatically since their evolutionary divergence from a common ancestor shared with chimpanzees. It seems reasonable to assume that a number of these changes were driven by positive Darwinian selection. However, although positive selection has been demonstrated for several human genes, the overall patterns of evolution of chimpanzee and human genes are consistent with selective neutrality. 4

There are two important points in this paragraph. The first sentence seems to imply something more like a 30/10 split rather than a 20/20 split because “humans have changed dramatically” compared to chimpanzees. If humans had 30 million mutations in 6 million years, and chimpanzees had 10 million mutations in 6 million years, then humans had an average of five mutations per year. In the last 4,000 years of recorded human history, there would have been about 20,000 mutations. Is there any evidence of that?

The more shocking statement in the paragraph quoted above is the one about natural selection. Evolution is supposed to work primarily through natural selection allowing positive changes to survive. But the nine authors of this peer-reviewed article think that most of the assumed changes in human DNA have no positive value. This makes natural selection an insignificant force in human evolution. If natural selection wasn’t the mechanism, what was?

Chimpanzees exist even though they don’t have the 40 million differences that humans have. So, those differences apparently aren’t necessary for survival. If creatures can survive with or without the differences, the changes are “neutral” as far as survival goes. But Darwin thought that “positive” differences, which promote survival, are the ones that drive evolution. That’s why some evolutionary scientists are looking for another method to explain evolution.

Looking for differences

Of course the primary reason for decoding the chimpanzee genome was to determine what differences make us “human.”

Perhaps we will learn how small differences in the code of life enabled us--but not chimpanzees--to cook soufflés, create symphonies, translate our own voyages into maps, build ever more complicated artifacts, and write plays that reflect the social intricacies of our lives. 5

Until now, genome sequence information has shown us how many seemingly very different organisms are amazingly like humans. At a conservative estimate we share about 88% of our genes with rodents and 60% with chickens. Applying a more liberal definition of similarity, up to 80% of the sea-squirt's genes are found in humans in some form. So it's no surprise that we are still asking, "What makes us human?" To apply genomics to this quest, we need to shift the focus to look at our closest living relative, the chimpanzee. Given that we share more than 98% of our DNA and almost all of our genes, chimps are the best starting point to study not the similarities, but the minute differences that set us apart. 6

The fact that one can fiddle with the numbers in such a way as to make the similarity between humans and sea squirts 80% is further proof that someone who is (conservatively) 88% rat can make the numbers say just about anything he wants.

But we really don’t want to quibble too much about the numbers. The important thing is to examine the similarities and differences between humans and chimps.

Before we tell you what differences the study found, why don’t you try to guess? Of all the organs shared by humans and chimpanzees, which do you think is the most different? We’re going to go out on a limb and say that you probably think that the study shows the biggest difference between chimps and humans is in the brain. If so, you are really, really wrong.

Two major findings stand out. First, gene expression patterns differ less between humans and chimpanzees in the brain than in the other tissues (bootstrap test, P < 0.0001). Second, the ratio of expression divergence between species to diversity within species is higher in testis than in any other tissue (5.6 versus 1.8 to 2.5, P < 0.0001). 7

So, they say, there is roughly three times more difference (5.6 to 1.8) in our testicles than in our brains. Let’s not go there!

Animal Intelligence

Scientists are appreciating more and more the intelligence of primates and other animals.

We now know that apes may actively encourage or deceive each other, transmit learned tool cultures, gang-kill rivals, or adopt motherless orphans. Above all, each is an individual who is politically astute or brutal, nurturing or careless, playing his or her own role in a complicated society. 8

Since Chandler discusses animals using tools in this month’s Evolution in the News column, “Animals Tooling Around”, we won’t say much about animal intelligence in this essay. We will simply note in passing that doctors can learn a thing or two from chimpanzees.

When chimpanzees are infected with certain pathogens, such as the nematodes that attack them in the Mahale Mountains of Tanzania, they consume plants that act as either chemical or physical defenses. For other ailments, including constipation, lethargy, and lack of hunger, they eat the bitter pith of a plant; this same plant is used across Africa as a local cure for humans infected with bilharzia and malaria. These discoveries, made possible by painstaking observations, have ignited an entire field of inquiry: searching for new remedies in the plant life that surrounds us. 9

Individual variations

When making comparisons of DNA sequences, we have to realize that there are limitations to the data.

… most of the chromosome 22 sequence has come from just one chimpanzee, it remains formally possible that some of the same polymorphisms also occur in chimp populations. 10

In other words, we know that there are differences in the DNA of different humans. The published human DNA genome is actually an average of several individuals. Each of those individuals differs by some percentage from the average. Unfortunately we have not been able to find out the actual percentage. In May, 2004, when the quote above was published, the DNA data came from only one chimp. We don’t know how many chimps were used in the genome that was published last month, nor do we know how much variation there is in the DNA of individual chimps. We are sure, however, that there is some variation. This diversity must certainly affect the 96% (or whatever percent) calculation.

But there is a more revealing statement about diversity in the most recent report.

Unfortunately, this pattern cannot be corroborated at the DNA sequence level because human DNA sequence diversity data collected in an unbiased way are not yet available. 11

What could this statement possibly mean? First, it seems to imply that results depend upon whose DNA is sequenced. If everyone’s DNA is exactly the same, it doesn’t matter whose DNA is used. But everyone’s DNA is somewhat different, and apparently it is different enough to affect the results. We don’t have a problem with this.

The disturbing phrase is “data collected in an unbiased way.” That implies that there is a way to collect data that would be biased to make the difference between humans and chimps appear more (or less) than it actually is; and that the biased method was the one that was used. So, we ask ourselves, “How could one bias the data?”

If one believes in evolution, and believes that some people have evolved farther from apes than other people, what would that imply about differences in DNA? Are the results unfairly biased because of the color of the skin of the people who supplied the samples? Surely, they don’t mean that! But if they don’t mean that, what do they mean?

What have we learned?

We could have told you what “scientists say” at the beginning of this essay; but if we had told you their conclusion right up front, there would have been no point in reading what we have to say. Here is what McConkey and Varki have concluded:

Can we now provide a DNA-based answer to the fascinating and fundamental question, "What makes us human?" Not at all! Comparison of the human and chimpanzee genomes has not yet offered any major insights into the genetic elements that underlie bipedal locomotion, a big brain, linguistic abilities, elaborated abstract thought, or any other unique aspect of the human phenome. 12

In all fairness, we need to say that the rest of the article we quoted above was a shameless plea for more money for research. One could argue that effective fundraisers never say, “We’ve got all the answers, now give us more money.” But that argument would rest on the assumption that scientists cast truth aside and say whatever they have to say to get more funding. Perish the thought! If one can’t believe what scientists say, what can one believe? But it isn’t just McConkey and Varki who have said that scientists haven’t found the answer yet.

Scientists produced a rough draft of the chimpanzee DNA sequence, and aligned it with the human one, and made an intimate comparison of the chimp and human genomes. "It's wonderful to have the chimp genome," says geneticist Mark Adams of Case Western Reserve University in Cleveland, Ohio, who was not on the papers. "It's the raw material ... to figure out what makes us unique."

But those hoping for an immediate answer to the question of human uniqueness will be disappointed. "We cannot see in this why we are phenotypically so different from the chimps," says Svante Pääbo of the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany, a co-author on one Nature paper and leader of a study in Science comparing gene expression in chimps and humans. 13

We still know what we always knew. Specifically, chimps look and act like humans more than other animals. Chimps’ DNA and internal organs (excluding one pair of external organs ) are very much like ours. But there is still no way to tell if that similarity is the result of descent from a common ancestor, or creation by a common designer.

It is sad to see how much time was wasted on calculating “average rates of evolution.” This time could have been better spent examining the differences and similarities, and what the results of these differences and similarities are. Humanity would have been better served if more time had been spent determining how the genetic differences between chimps and humans affect susceptibility to disease. More time could have been spent studying the compounds in healing herbs that chimpanzees eat when they are sick.

The biggest threat to science education in America is the theory of evolution, which wastes the time and intelligence of some of our best scientists.

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1 Elizabeth Culotta, Science, Vol. 309, 2 September 2005, “GENOMICS: Chimp Genome Catalogs Differences With Humans”, pages 1468-1469, https://www.science.org/doi/10.1126/science.309.5740.1468 (Ev)
2 ibid.
3 Carina Dennis, Nature 437, 1 September 2005, “Chimp genome: Branching out”, pages 17-19, https://www.nature.com/articles/437017a (Ev)
4 Philipp Khaitovich, Ines Hellmann, Wolfgang Enard, Katja Nowick, Marcus Leinweber, Henriette Franz, Gunter Weiss, Michael Lachmann, Svante Pääbo, Science, Vol 309, 16 September 2005, “Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees”, pages 1850-1854, https://www.science.org/doi/10.1126/science.1108296 (Ev)
5 Marc D. Hauser, Science, Vol. 309, 2 September 2005, “NATURAL HISTORY: Beyond the Chimpanzee Genome: The Threat of Extinction”, pages 1498-1499, https://www.science.org/doi/10.1126/science.1111421 (Ev)
6 Chris Gunter and Ritu Dhand, Nature 437, 1 September 2005, "The chimpanzee genome", https://www.nature.com/articles/437047a (Ev)
7 Philipp Khaitovich, Ines Hellmann, Wolfgang Enard, Katja Nowick, Marcus Leinweber, Henriette Franz, Gunter Weiss, Michael Lachmann, Svante Pääbo, Science, Vol 309, Issue 5742, pages 1850-1854, 16 September 2005, “Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees”, https://www.science.org/doi/10.1126/science.1108296 (Ev)
8 Alison Jolly, Science, Vol. 309, 2 September 2005, “The Last Great Apes?”, page 1457, https://www.science.org/doi/10.1126/science.1111873 (Ev)
9 Marc D. Hauser, Science, Vol. 309, 2 September 2005, “NATURAL HISTORY: Beyond the Chimpanzee Genome: The Threat of Extinction”, pages 1498-1499, https://www.science.org/doi/10.1126/science.1111421 (Ev)
10 Jean Weissenbach, Nature, Vol. 429, May 2004, “Differences with the relatives”, page 353, https://www.nature.com/articles/429353a (Ev)
11 Philipp Khaitovich, Ines Hellmann, Wolfgang Enard, Katja Nowick, Marcus Leinweber, Henriette Franz, Gunter Weiss, Michael Lachmann, Svante Pääbo, Science, Vol 309, Issue 5742, pages 1850-1854, 16 September 2005, “Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees”, https://www.science.org/doi/10.1126/science.1108296 (Ev)
12 Edwin H. McConkey and Ajit Varki, Science, Vol. 309, 2 September 2005, “GENOMICS: Thoughts on the Future of Great Ape Research”, pages 1499-1501, https://www.science.org/doi/10.1126/science.1113863 (Ev)
13 Elizabeth Culotta, Science, Vol. 309, 2 September 2005, “GENOMICS: Chimp Genome Catalogs Differences With Humans”, pages 1468-1469, https://www.science.org/doi/10.1126/science.309.5740.1468 (Ev)